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Improve safety of NER build #127

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merged 2 commits into from
Feb 6, 2024
Merged

Improve safety of NER build #127

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674402b
Improve safety of NER build
cthoyt Jan 2, 2024
7b72202
Update term.py
cthoyt Feb 5, 2024
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4 changes: 4 additions & 0 deletions gilda/grounder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,11 @@ def __init__(
def _build_prefix_index(self):
prefix_index = defaultdict(set)
for norm_term in self.entries:
if not norm_term:
continue
parts = norm_term.split()
if not parts:
continue
prefix_index[parts[0]].add(len(parts))
self.prefix_index = dict(prefix_index)

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2 changes: 2 additions & 0 deletions gilda/term.py
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Expand Up @@ -52,6 +52,8 @@ def __init__(self, norm_text, text, db, id, entry_name, status, source,
organism=None, source_db=None, source_id=None):
if not text:
raise ValueError('Text for Term cannot be empty')
if not norm_text.strip():
raise ValueError('Normalized text for Term cannot be empty')
self.norm_text = norm_text
self.text = text
self.db = db
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